Open Access Highly Accessed Research

Microbiome dynamics of human epidermis following skin barrier disruption

Patrick LJM Zeeuwen12, Jos Boekhorst134, Ellen H van den Bogaard12, Heleen D de Koning12, Peter MC van de Kerkhof2, Delphine M Saulnier4, Iris I van Swam4, Sacha AFT van Hijum134, Michiel Kleerebezem45, Joost Schalkwijk12* and Harro M Timmerman4*

Author Affiliations

1 Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen Medical Centre, PO BOX 9101, 6500 HB Nijmegen, The Netherlands

2 Nijmegen Institute for Infection, Inflammation and Immunity (N4i), Radboud University Nijmegen Medical Centre, PO BOX 9101, 6500 HB Nijmegen, The Netherlands

3 Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen Medical Centre, PO BOX 9101, 6500 HB Nijmegen, The Netherlands

4 NIZO Food Research B.V., Kernhemseweg 2, 6718 ZB, Ede, The Netherlands

5 Wageningen University, Host-Microbe Interactomics Group, De Elst 1, 6708 WD, Wageningen, The Netherlands

For all author emails, please log on.

Genome Biology 2012, 13:R101  doi:10.1186/gb-2012-13-11-r101

Published: 15 November 2012

Additional files

Additional file 1:

Table showing microbiome analysis of 4 different body locations (N = 5).

Format: PDF Size: 56KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Microbial community composition of upper buttock skin and forehead. Relative abundances of the most abundant bacterial taxa on (A) upper buttock, and (B) forehead. The figure illustrates the average composition of the sample for different levels of bacterial taxonomy, from the domain level (left) to the genes level (right). Figure generated using software described in Sundquist et al [69], also providing or more detailed description of the visualization.

Format: PDF Size: 996KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Experimental set-up tape-stripping upper buttock skin. On the right site the experiment is depicted that was used to study the human skin microbiome in different epidermal layers. Two areas on the right upper buttock measuring 2 cm2 (1 × 2 cm) each, were tape-stripped 5 (STR5) and 10 (STR10) times respectively by application and removal of adhesive tape (n = 12, F1-6 and M1-6). Subsequently, barrier disrupted skin areas were sampled, as well as 2 cm2 healthy non-barrier disrupted right upper buttock skin (STR0). To study recolonization of the human skin microbiome after skin barrier disruption, four areas on the left upper buttock measuring 2 cm2 each, were tape-stripped 15 times (n = 6, F1-3 and M1-3) or as many times as required to obtain a glistening surface which indicates complete removal of the stratum corneum (F4-6 and M4-6).

Format: PDF Size: 442KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Table with read and OTU counts.

Format: PDF Size: 59KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Clustering and microbial community composition of different volunteers and recolonization in time. Samples were clustered using UPGMA with weighted UniFrac as a distance measure. The figure was generated with iTOL [70]. Composition is displayed as relative abundance, i.e. the number of reads assigned to a genus divided by the total number of reads assigned up to the genus level. Sample names with the same color come from the same volunteer (M = male1 to 6, F = female1 to 6), followed by the time of recolonization (t = 1, 3, 7 or 14 days). STR0 is normal, healthy skin (not tape-stripped). Colored bars represent the relative abundance of bacterial genera as determined by barcoded pyrosequencing.

Format: PDF Size: 252KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Morphology of tape-stripped skin and subsequent regeneration of human epidermis. (A) H&E staining of normal healthy skin. (B) The stratum corneum which is present in normal skin has been stripped off completely (biopsy taken 2 hours after tape-stripping). (C) A picture taken 4 hours after tape-stripping showing more hypertrophic basal cells, several pyknotic nuclei in cells of the stratum spinosum, and a layer of parakeratotic cells that begins to form on the surface. (D) At the stage of 24 hours after tape-stripping the basal cells are really hypertrophic and these columnar basal cells make up about one third of the thickness of the epidermis. Hyperparakeratosis is observed on top of the epidermis. (E) Pronounced acanthosis and hyperparakeratosis is seen after 48 hours. At this stage the tape-stripping skin model resembles most lesional psoriatic skin. (F) Finally at 96 hours, the hyperparakeratosis is disappeared and a fresh anuclear stratum corneum is formed on the emerging stratum granulosum. Scale bar = 100 μm.

Format: PDF Size: 989KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Relative abundance of all detected genera in females (A) and males (B) of the deeper skin layer (STR10) compared to the recolonizing skin in time (DAY 1, 3, 7 and 14).

Format: PDF Size: 727KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 8:

Topographical distribution of bacteria on skin sites on the back. The upper buttock skin contains a high bacterial diversity (data from the present study) and its microbial composition is intermediate between the microbiome of the back between the scapulae and the lower buttock as published by Grice et al [18]. Moist sites are labeled in green, sebaceous sites are labeled in blue, and dry surfaces in red. The upper buttock is labeled in purple.

Format: PDF Size: 3.1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9:

Yield bacterial genomic DNA after tape-stripping. Swabs were taken from upper buttock skin and from skin that was tape-stripped 1, 10, 15, and 30 times on this part of the body. Genomic DNA was extracted using the Mobio Ultraclean Microbial DNA Isolation Kit and concentrations were determined by real-time qPCR using broad range universal primers targeting the 16S rRNA gene [71] and calculated from a standard dilution series of Staphylococcus epidermidis.

Format: PDF Size: 169KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 10:

Exclusion criteria. Description of the exact inclusion/exclusion criteria.

Format: PDF Size: 15KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 11:

Study procedures. Description of the study procedures presented to the volunteers.

Format: PDF Size: 51KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 12:

Participation of volunteers. Specification of which volunteers participated in the different studies.

Format: PDF Size: 55KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 13:

Supplementary methods. The text outlines the different statistical tools used in our analysis.

Format: PDF Size: 84KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 14:

Table with qPCR primer sequences and efficiency.

Format: PDF Size: 73KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data